Pinus taeda has historically large, interconnecting populations which extend along the US Atlantic seaboard from Maryland to Florida and westward to central Texas. Genetic divergence is greatest east and west of the Mississippi River Valley but there are no estimates of allelic diversity or diagnostic alleles. To test allelic diversity and detect diagnostic alleles, samples were drawn from grafted archives of natural stand selections from 1950 to 1970. The samples represented P. taeda prior to intensive plantation establishment and domestication. The eastern range had higher mean allelic diversity than western populations (10 versus 8.5 alleles per locus) even after adjustment for sample size and geographic area. A total of 46 unique alleles were detected; nine were considered diagnostic. There were more diagnostic alleles east of the Mississippi River Valley compared to the western part of the species' range. Gene flow estimates for P taeda were high, ranging from two to six migrants per generation per population. Cross-validation using Mississippi and Alabama samples supported the gene flow patterns, showing an admixture at the juncture of the Mississippi River Valley. Lower allelic diversity in the western range of P. taeda and higher number of diagnostic alleles in the eastern range are attributed to (1) a prevailing wind direction which facilitates viable pollen movement from west to cast, and (2) a gradual contraction in western R taeda population sizes over the past 5000-8000 years. (C) 2002 Elsevier Science B.V. All rights reserved.